The long-term goal of this project is to understand the genetic mechanisms and evolutionary processes responsible for generating phenotypic diversity within and between species. This includes discovering the genes responsible for phenotypic divergence, identifying which changes within these genes affect the phenotype, and determining how these changes alter molecular, cellular, and developmental processes. It also includes figuring out how mutation and selection have worked together to give rise to these changes. These goals will be accomplished by combining methods from developmental biology, population and quantitative genetics, molecular evolution, bioinformatics and genomics to study both fruit flies (Drosophila) and yeast (Saccharomyces). Specific experiments proposed are designed to address the following four complementary questions: (1) What are the genetic and molecular mechanisms underlying phenotypic differences and how did they evolve? (2) How do cis-regulatory sequences determine gene expression and how does their architecture change over time? (3) How do regulatory networks composed of cis- and trans-acting factors evolve and account for changes in gene expression? and (4) What are the functional properties of new regulatory mutations and how do they influence regulatory variation? Taken together, this work will advance our understanding of genotype-phenotype maps and how they vary within and between species. Genetic changes affecting the regulation of gene expression, an essential step in translating genotypes into phenotypes, will be given particular emphasis in this work. Ultimately, lessons learned from these studies will contribute to a general framework for predicting and interpreting patterns of genotypic and phenotypic variation related to health in human populations.